title: Analysis of deficiency of adenosine deaminase 2 pathogenesis based on single cell RNA sequencing of monocytes

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

summary:
Background and methods: Deficiency of adenosine deaminase 2 (DADA2) is a rare autosomal recessive disease caused by loss-of-function variants in the ADA2 gene. DADA2 typically presents in childhood and is characterized by vasculopathy, stroke, inflammation, and immunodeficiency as well as hematologic manifestations. The ADA2 protein is predominantly expressed in stimulated monocytes, dendritic cells, and macrophages. To elucidate molecular mechanisms in DADA2, CD14+-monocyte expression of 14 patients and 6 healthy donors were analyzed using single cell RNA sequencing (scRNA-seq).
Results: By comparing gene expression of each monocyte subtypes between patients and healthy donors, we identified upregulation of immune response pathways.
Conclusion: Our results suggest that responses to stimulie are upregulated and protein synthesis is reduced in order to cope with aberrant immune responses. Our findings would contribute to elucidate pathogenesis of this disease.

overall_design: RNA profiles of single peripheral blood monocytes of 14 DADA2 patients and 6 healthy donors were generated by deep sequencing using quencing using Illumina HiSeq 3000

first: Naoki

last: Watanabe


title: Identification of miRNA expression profiles following traumatic spinal cord injury by  high-throughput sequence analysis [miRNA]

status: Public on Oct 27 2021

city: Jinan

first: Bin

last: Ning

address: Jiefang Road #105

country: China

institute: Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: To systematically profile and characterize miRNA expression pattern in the lesion  epicenter of spinal tissues after traumatic spinal cord injury (TSCI). We used RNA-Seq to profle the expression and regulation patterns of miRNAs of mice  models after TSCI. A total of 155 miRNAs were identified in TSCI mice  models to be differentially expressed.

overall_design: Spinal cord miRNA profiles of 8-week old C57BL/6 mice with/without traumatic spinal cord injury

first: Jianan

last: Chen

first: Wenzhao

last: Wang

first: Yanlin

last: Su


title: Genome-wide DNA methylation profiles of Arsenic exposed subjects through drinking water in Pakistan

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

type: Methylation profiling by genome tiling array

summary: Ground water Arsenic (As) toxicity is a global problem and millions of people are exposed to elevated levels (more than WHO advised maximum limit of 10µg/L) through drinking water. The exposure is associated with various cancerous and non-cancerous diseases. It may alter DNA methylation profiles of inviduals and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also has reported elevated ground water As levels in various investigations since 2005. However, a very limited biomonitoring studies have been conducted in this context while no study reports molecular changes associated with drinking water As exposure in Pakistan. Within this context, the present study aimed to investigate genome-wide DNA methylation profiles of the exposed subjects in two districts of Punjab Province Pakistan, i.e Lahore and Kasur. The population was stratified into three exposure groups comprising Low, Medium and High exposure based on their urinary arsenic levels. Genome-wide DNA methylation profiles were obtained using MeDIP in combination with NimbleGen 2.1M Deluxe Promotor arrays.

overall_design: Freshly taken blood samples were collected form the respective exposure groups and transported in dry ice to Department of Toxicogenomics Maastricht University, The Netherlands for further analysis. DNA was isolated from buffy coats for performing global DNA methylation analysis using Methylated DNA immunoprecipitation (MeDIP-CHIP) on NimbleGen 2.1M Deluxe Promotors arrays (Roche, NimbleGen).

first: Muhammad

middle: Y

last: Rehman

first: Jos

middle: C

last: Kleinjans

first: Jacco

middle: J

last: Briedé

first: Marcel

last: van Herwijnen

first: Julian

last: Krauskopf

middle: G

first: Riffat

middle: N

last: Malik


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [ChIP-seq]

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Skeletal muscle satellite cells (SCs) are muscle stem cells responsible for muscle development and injury induced muscle regeneration. The pace of SC related study, however, is constrained partially by the technological limitations in generating genetically modified mice. Although the ease of use of CRISPR-Cas9 in genome manipulation has been documented in many cell lines and various species, its application in endogenous SCs remains elusive. In this study, we generated muscle-specific Cas9-expressing mice and achieved robust in vivo genome editing in juvenile SCs at the postnatal stage through AAV9 mediated short guide RNAs (sgRNAs) delivery. We also found adult quiescent SCs are reluctant to CRISPR/Cas9 editing despite efficient AAV9 transduction. To edit juvenile SCs in vivo, as a proof-of-concept, we delivered sgRNAs targeting MyoD, a key gene critical for muscle physiology and showed an efficient editing at MyoD locus, resulting in accumulation of SCs and defects in SCs differentiation which resembled the phenotypes reported in MyoD knockout mice. Further application of this system on potential key transcription factors (TFs) involved in SC fate transition, Myc, Bcl6 and Pknox2, unveiled their distinct functions in the early stage of SC activation and injury induced muscle regeneration. In addition, we revealed that Myc orchestrated SCs activation through impinging on 3D chromatin architecture. Altogether we established a robust muscle restricted CRISPR/Cas9-based gene editing platform in endogenous SCs and elucidated the functionality of key factors governing SC activities.

overall_design: H3K27ac ChIP-seq was performed in freshly isaloted or activated muscle stem cells.

first: Wang

last: Huating

first: Sun

last: Hao

first: He

last: Liangqiang

first: So

middle: K

last: Karl

first: Ding

last: Yingzhe


title: RNA-seq analysis of human antigen-specific type 1 regulatory T cells (Tr1)

city: Stanford

first: Alma-Martina

last: Cepika

state: CA

address: 265 Campus Drive West

department: Pediatrics

country: USA

institute: Stanford University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Co-culture of human CD4+ T cells with allogeneeic tolerogenic dendritic cells (DC-10) results in a cell product, called T-allo10, enriched with alloantigen-specific type 1 regulatory T cells (Tr1 cells). CD49b+LAG3+ Tr1 cells and CD49b-LAG3- non-Tr1 cells (DN) were sorted from total T-allo10 cells, and their transcriptomes compared to parental CD4+ T cells, as well as to and control CD49b-LAG3- effector T cells (Teff) sorted from T-allo cells, which were made equivalently to T-allo10 except with using mature dendirtic cells instead of DC-10.

overall_design: Tr1 cells compared to all not-Tr1 cells (DN, CD4, Teff)


title: Role of transcription factors ONECUT1 (HNF6), GATA6 and NKX6.1 during in vitro pancreatic differentiation of human pluripotent stem cells.

city: Aachen

first: Ivan

last: Costa

address: Pauwelsstraße 19

country: Germany

institute: Unikilink RWTH Aachen

summary:
We have identified HNF6 as an essential transcription factor for endocrine pancreatic development.
HNF6 binds to and possibly regulates other isletogenesis transcription factors, driving endocrine differentiation.
ChIP sequencing of HNF6 as well as GATA6 and NKX6.1 during in vitro pancreatic differentiation will help to understand the regulatory mechanisms during cell fate decisions.

overall_design: The human embryonic stem cell line CyT49 differentiated to gut tube endoderm and pancreatic progenitor cells were used for chromatin immunoprecipitation.

first: Gino

last: Kwon

first: Zhijian

last: Li

first: Alexander

last: Kleger

first: Sandra

last: Heller


title: Role of transcription factor ONECUT1 (HNF6) during in vitro pancreatic differentiation of human pluripotent stem cells [ATAC-seq]

summary:
We have identified HNF6 as an essential transcription factor for endocrine pancreatic development.
HNF6 binds to and possibly regulates other isletogenesis transcription factors, driving endocrine differentiation.
ATAC sequencing of control and HNF6-depleted hESC during in vitro pancreatic differentiation will help to understand the regulatory mechanisms during cell fate decisions.

overall_design: The human embryonic stem cell line HUES8 differentiated to definitive endoderm, gut tube,  pancreatic endoderm and pancreatic progenitor cells was used for ATAC sequencing.


title: Multiomics profiling of HIV-infected cells

status: Public on Oct 26 2021

city: ATLANTA

first: Stefan

middle: G.

last: Sarafianos

state: GA

address: 1760 Haygood Drive NE

institute: Emory University School of Medicine

summary: The restructuring of chromatin architecture following lentiviral integration is not well elucidated. We jointly interrogate (HIV-distal & -local) chromatin organization (via Hi-C & ATAC-seq) and the RNA landscape around defined sites of proviral integration using HIV-inducible cellular models. We report chromatin interaction networks and nuclear ultrastructure around integrated HIV-1 are predominantly preserved, suggesting HIV integration does not induce large scale remodeling of cellular chromatin. Instead, we find that induction of proviral transcription leads to stark local changes in nucleosome organization with chromatin accessibility increasing at the intergenic junction between the HIV-1 3’ LTR and flanking cellular genome. This result suggests subtle changes in chromatin structure may be mediating proviral activation. Using long-read Nanopore RNA-seq, we interrogate the local host & HIV transcriptomes, observing a small fraction of HIV-1 transcripts are chimeric read-through products, where transcription initiates at the HIV-1 5’ LTR promoter and continues extensively into the flanking cellular genome. Despite provirus-driven read-through, HIV-1 appears to have only a modest effect on the local transcriptional environment. The changes in chromatin accessibility and read-through at activated proviruses closely resembles lytic Herpes simplex virus type 1 (HSV-1) induced cellular chromatin reprogramming. We propose chromatin “opening” at the 3’ LTR HIV-host junction is important for sustained proviral activity, and overall, HIV proviruses do not significantly alter local host transcription and chromatin structure. Our studies provide the first in-depth integrative investigation of 3D chromatin organization, nucleosome density, and HIV-host transcriptomes at HIV-host genic boundaries.

overall_design: Chromatin and gene expression profiling at HIV-1 sites of integration in HIV-inactive -active states

first: Raven

last: Shah

first: Yoonhee

middle: H

last: Jung

first: Victor

last: Corces


title: Gene expression by Aspergillus protease

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: This study was designed to measure the gene expression profile of human primary bronchial epithelial cells treated with Aspergillus protease.

overall_design: Expression of genes induced by Aspergillus protease in human primary bronchial epithelial cells was measured by time after treatment. Total RNA was isolated and was subject to single channnel microarray.


title: Identification of a Choroid Plexus Vascular Barrier Closing during Intestinal Inflammation to Protect the Brain

city: Rozzano (MI)

first: Daniele

last: Braga

address: Via Manzoni 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis I

city: Guangzhou

first: hongling

last: guan

address: tianhe

institute: South China Agricultural University

summary: Litchi possesses unique ﬂower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower organ development remains largely unknown. MADS-box genes are promise candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes, and can be divided into type I and type II genes. Fifty type I MADS-box genes are sub-divided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC*-type genes. Both two types of LcMADS genes mainly contain ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveals that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes including LcMADS42/46/47/75/93/100 play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS75 (LcAP1) and LcMADS51 (LcSTK). However, JA probably plays a negative role in litchi flower development.

overall_design: Analysis of MADS-box gene expression in the floral organs of three types of litchi flowers

first: Houbin

last: Chen

first: Jiyuan

last: Shen

first: Hongling

last: Guan


title: Identification of a Choroid Plexus Vascular Barrier Closing during Intestinal Inflammation to Protect the Brain [scRNA-Seq]

summary: Profiles of the cellular components of the CP at single cell resolution (via 10X scRNA-seq) during the preclinical murine model of DSS ulcerative colitis

overall_design: Lateral ventricles CP of five adult mice (untreated and T1, T3 DSS treated) were microdissected and pooled together. One sample, containing 5 biological replicates was used for the subsequent sequencing. Approximately 7000 cells from each sample were loaded into Single Cell Chip B (10X Genomics,#PN-1000092) using the Single Cell 3’ v3 reagent kit (10X Genomics, # PN-1000074) for gel bead emulsion generation in the Chromium system.

first: Sara

last: Carloni

first: Maria

last: Rescigno

first: Daniel

last: Fernandez-Perez

first: Diego

last: Pasini


title: Efficient arming of memory-like NK cells with a TCR-like CAR for treating acute myeloid leukemia with NPM1 mutation

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: We showed Cytokine induced memory-like (CIML) human NK cells have higher trasduction efficiency with CAR lentivirus for therapeutics. We performed single cell RNAseq analysis to comprehensively understand the transcripttion difference between NPM1c-CAR-mb15 CIML NK cells and CAR-negative CIML NK cells, as well as their transcriptional response to NPM1c+ AML tumor cells.

overall_design: CIML NK cells were generated from purified NK cells from human PBMC (two different donors) in vitro and then transduced with NPM1c-CAR-mb15 lentivirus. Single cells (mixture of transduced and non-transduced)  post 5 days transduction were immmediately applied to single cell RNAseq. At the same time, CIML NK cells were cocultured with OCI-AML3 target tumor cells for 24 hrs and then applied to single cell RNAseq.

first: Jianzhu


title: Krüppel-like Factor 5 Regulates Stemness, Lineage Specification, and Regeneration of Intestinal Epithelial Stem Cells

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Intestinal stem cells are required for proliferation, differentiation, and regeneration of the intestinal epithelium. Krüppel-like factor 5 regulates intestinal stem cells in both physiologic and pathological conditions and may be a treatment target in certain diseases of the intestine.

overall_design: ChIP-seq analysis of control mouse intestinal stem cells and Klf5-deleted intestinal stem cells.

first: Chang-Kyung

first: Madhurima

last: Saxena

first: Kasmika

last: Maharjan

first: Jane

last: Song

first: Kenneth

middle: R

last: Shroyer

first: Agnieszka

middle: B

last: Bialkowska

middle: A

first: Vincent

middle: W

last: Yang


title: Genome wide expression change by C4-2 cells treated with MST1/2 inhibitor XMU-MP-1

city: Xinxiang

first: Ting

last: Zhuang

state: Henan

address: Jinsui Road 601

institute: Xinxiang Medical University

summary: We aim to the investigate the role of MST1/2 inhibitor XMU-MP-1 in prostate cancer progression. C4-2 cells were used as the model.

overall_design: The C4-2 cells were treated with vehicle or 3 μM XMU-MP-1 . After 6 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Shu

last: Zhuo

first: Jian

last: Zhu

first: Jin

last: Jiang


title: Identification of driver genes for severe forms of COVID-19 in a deeply phenotyped young patient cohort

first: Richard

last: Li

address: 90 Canal St, Suite 120

department: GAIRI

institute: Genuity Science

summary: The etiology of severe forms of COVID19, especially in young patients, remains a salient unanswered question. Here we build built on a 3-tier cohort where all individuals/patients were strictly below 50 years of age and where a number of comorbidities were excluded at study onset. Besides healthy controls (N=22), these included patients in the intensive care unit with Acute Respiratory Distress Syndrome (ARDS) (“critical group”; N=47), and those in a non-critical care ward under supplemental oxygen (“non-critical group”, N=25). This highly curated cohort allowed us to perform a deep multi-omics approach, which included whole genome sequencing, whole blood RNA-sequencing, plasma and peripheral-blood mononuclear cells proteomics, multiplex cytokine profiling, mass-cytometry-based immune cell profiling in conjunction with viral parameters i.e. anti-SARS-Cov-2 neutralizing antibodies and multi-target antiviral serology. Critical patients were characterized by an exacerbated inflammatory state, perturbed lymphoid and myeloid cell compartments, signatures of dysregulated blood coagulation and active regulation of viral entry into the cells. A unique gene signature that differentiates critical from non-critical patients was identified by an ensemble of machine learning, deep learning and quantum annealing approachmethods. Within this gene networksignature, Sstructural Causal causal Modeling modeling identified several genes that may potentially drivepromote ARDS driver genes etiology, among which the up-regulated metalloprotease ADAM9 seems to be a key driver. Inhibition of ADAM9 ex vivo interfered with SARS-Cov-2 uptake and replication in human epithelial cells. In brief, Hence we applyied an advanced integrated machine learning approach and probabilistic programming strategy to identify causal molecular driver geness for of severe forms of COVID-19 in a small, uncluttered tightly controlled cohort of patients, the importance of which were then validated with experiments.

overall_design: RNA-seq was performed on 69 whole blood RNA samples corresponding to 46 critical and 23 non-critical patients at hospitalization.

first: Raphael

last: Carapito


title: RIPK1 dephosphorylation and kinase activation by PPP1R3G/PP1γ promote apoptosis and necroptosis

city: Dallas

first: Zhigao

last: Wang

state: TX

address: 5323 Harry Hines Blvd., NA8.202

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Receptor-interacting protein kinase 1(RIPK1) is a key regulator of inflammation and cell death. Many sites on RIPK1, including serine 25, are phosphorylated to inhibit its kinase activity and cell death. How these inhibitory phosphorylation sites are dephosphorylated is poorly understood. Using a sensitized CRISPR whole genome knockout screen, we discover that protein phosphatase 1 regulatory subunit 3G (PPP1R3G) is required for RIPK1-dependent apoptosis and necroptosis. Mechanistically, PPP1R3G recruits its catalytic subunit protein phosphatase 1 gamma (PP1g) to Complex I to remove inhibitory phosphorylations of RIPK1. A PPP1R3G mutant which does not bind PP1g fails to rescue RIPK1 activation and cell death. Furthermore, chemical prevention of RIPK1 inhibitory phosphorylations or mutation of serine 25 of RIPK1 to alanine largely restores cell death in PPP1R3G-knockout cells. Finally, Ppp1r3g-/- mice are protected from tumor necrosis factor-induced systemic inflammatory response syndrome, confirming the important role of PPP1R3G in regulating apoptosis and necroptosis in vivo.

overall_design: To identify genes required for necroptosis through CRISPR mediated whole-genome knockout screen in modified HAP1 haploid cells

first: Yougui

last: Xiang

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: Tumor-infiltrating, adoptively transferred BATF-overexpressing CD8 T cells analyzed via bulk RNA-seq

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: In cancer, tumor infiltrating lymphocytes (TILs) often differentiate into dysfunctional states, re-sembling exhausted T cells that arise in chronic viral infections. The dysfunctional state of exhaustion in CD8 T cells is characterized by diminished effector function, namely decreased cytotoxic activity and reduced expression of effector molecules, such as granzyme B. BATF is a transcription factor (TF) known to promote the differentiation of effector CD8 T cells in the chronic viral infection model; however, its role in cancer is not well studied. Using bulk RNA-sequencing (bulk RNA-seq), we identified that BATF-overexpression in tumor-specific CD8 T cells exhibited enrichment for a gene set upregulated in early effector CD8 T cells compared to late exhausted CD8 T cells. Notably, BATF overexpression enhanced the gene expression of various activation markers, costimulatory molecules, effector molecules, chemokine receptors, and other transcription factors, including Hif1a. Additionally, GSEA analysis revealed that BATF-overexpressing CD8 T cells were negatively enriched for Reactome pathways of cellular responses to stress as well as stress-induced senescence. Collectively, our findings support BATF as a key regulator of effector CD8 T cell activity and function within the tumor and shed light on potential pathways BATF may upregulate to facilitate effective tumor control.

overall_design: 5 replicates of two treatment groups of tumor-bearing mice received adoptive cell transfer of Pmel CD8 T cells retrovirally-expressing either MIT-BATF or MIT-empty vector control.

first: Paytsar

last: Topchyan

first: Moujtaba

last: Kasmani


title: Transcriptome of stem cell derived hepatocytes and hepG2 cells under conditions of amino acid supplementation

city: Leuven

first: RUBEN

last: BOON

state: Vlaams Brabant

address: Herestraat 49

country: Belgium

institute: KU LEUVEN

summary: We report that the addition of high amounts of amino acids, combined with the overexpression of transcription factors, results in a shift of the global transcriptome of both stem cell derived hepatocytes and HepG2 cells towards the profile of primary human hepatocytes,

overall_design: HepG2 cells were either grown for 5 days in standard DMEM 10% FBS medium, or in medium suppelmented with high amounts of amino acids. Stem cell derived hepatocyets were differentiated towards the hepatic lineage without (HLC) or with the overexpression of 3 (HC3X) or 6 (HC6X) transcription factors, and this in standard medium or in medium supplemented with high levels of amino acids.

first: Ruben

last: Boon


title: RNASeq of murine choroid plexus following one (T1), three (T3) and three days of DSS treatment followed by two days of water (T5)

first: Daniele

last: Braga

summary: To evaluate, at the molecular level, potential pathways involved in changes of PVB permeability, we dissected lateral CP tissues at all time points (T0, T1, T3, or T5) and performed transcriptional profiling by deep RNA-sequencing. We used a regression model-based method for the classification of co-regulated genes based on their temporal expression profiles and the identification of differentially expressed genes (DEGs).

overall_design: The experiment includes 4 groups: CTRL (n=5), T1 (n=4), T3 (n=4), T5 (n=4)

first: Sara

last: Carloni

first: Maria

last: Rescigno


title: RNA-seq of mouse colon tissue treated with engineered IL-22 variants

first: Robert

last: Saxton

address: 279 Campus Drive, Beckman Center, Room B173

department: Department of Molecular & Cellular Physiology

institute: Stanford University

summary: RNA-seq analysis of colon tissue from mice treated with PBS, WT IL-22, or engineered IL-22 variant 22-B3.

overall_design: Mice were administered PBS, WT IL-22 (200 ug) or 22-B3 (200 ug) for six hours.

first: K

last: Garcia


title: The Long Terminal Repeats of ERV6 Are Activated in Pre-Implantation Embryos of Cynomolgus Monkey

status: Public on Oct 25 2021

city: Kunming

first: Tianqing

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: Kunming University of Science and Technology

summary: Precise temporal development is an important event during embryo development. However, transcriptional changes in the temporal development of early epiblast cells (EPI), primitive endoderm (PrE) and trophectoderm (TrB) cells remain unclear. Long terminal repeat elements (LTRs) of ERVs (Endogenous retroviruses) are dynamically expressed in blastocysts of mammalian embryos. However, the expression of LTRs in monkey blastocyst is still unknown. By analyzing publicly available single-cell RNA-sequencing (seq) data, LTRs of several ERV families, including MacERV6, MacERV3, MacERV2, MacERVK1 and MacERVK2 were highly expressed in pre-implantation embryo cells including EPIs, TrB and PrE but absent in post-implantation. We knockdown MacERV6-LTR1a in cynomolgus monkey with short hairpin RNA (shRNA) strategy to examine the potential function of MacERV6-LTR1a in early development of monkey embryo. The silence of MacERV6-LTR1a mainly postpone trophectodermal cell differentiation and cell polarity of TrB, and the genes relate to epithelial proliferation, differentiation and development were downregulated in EPI of shRNA-treated embyos. Addtionally, stem cell differentiation relate genes were downregulated in PrE when MacERV6-LTR1a was silenced. Moreover, we have comfirmed MacERV6-LTR1a can recruit ESRRB (Estrogen Related Receptor Beta). Actually, recent reports demonstrated that ESRRB plays a important role in maintenance of self-renewal and pluripotency of embryonic and trophoblast stem cells through different signaling pathways including FGF and Wnt signaling pathways. In summary, these results suggest that MacERV6-LTR1a potentially regulates the temporal development of pre-implantation embryo of cynomolgus monkey.

first: Kui

last: Duan

first: Yun

last: Zheng


title: Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN (RNA-Seq)

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Neuroblastoma cell identity depends on a core regulatory circuit (CRC) of transcription factors that incorporate MYCN to drive the oncogenic gene expression program. For neuroblastomas dependent on the adrenergic CRC, treatment with retinoids can inhibit cell growth and induce differentiation in both primary neuroblastomas and cell lines; however, the underlying mechanisms remain unclear. Here we show that when MYCN-amplified neuroblastomas cells are treated with all-trans retinoic acid (ATRA), they undergo modifications of histone H3K27 acetylation and methylation that decommission super-enhancers driving the expression of PHOX2B and GATA3, together with the activation of new super-enhancers that drive high levels of expression of MEIS1, HIC1 and SOX4. These findings indicate that treatment with ATRA can reprogram the enhancer landscape to collapse the adrenergic CRC, which downregulates MYCN expression, while upregulating a new “retino-sympathetic” CRC that causes proliferative arrest and sympathetic differentiation.  Thus, we provide mechanisms that account for the beneficial effects of retinoids against high-risk neuroblastoma and explain the rapid downregulation of expression of MYCN despite massive levels of gene amplification.

overall_design: RNA-seq in neuroblastoma cell lines treated with all-trans retinoic acid

first: Mark

last: Zimmerman

first: Adam

middle: D

last: Durbin

first: Shuning

last: He

first: Alla

last: Berezovskaya

first: Felix

last: Oppel

first: Hui

last: Shi

first: Ting

last: Tao

first: Zhaodong

last: Li

first: Yu

last: Liu

first: Jinghui

last: Zhang

first: Brian

last: Abraham

first: A

middle: T

last: Look


title: Single cell RNA sequencing of mice skin cells in DMBA/TPA-induced tumorigenesis model

city: tsukuba

first: Yuho

last: Nakamura-Shinya

state: ibaraki

address: Ibaraki, tuskuba city, tennodai1-1-1

country: Japan

institute: univesity oftsukuba

summary: WT or Cd226-/- mice were treated with DMBA and TPA. Three weeks later, cells were isolated from mice back skin, and divided CD45+ and CD45- cells by cell sorter. CD45+ and CD45- cells were mixed in 1:1 ratio, and we performed scRNA sequencing of skin cells.

overall_design: WT or Cd226-/- mice on the BALB/c background were treated with DMBA and TPA. Three weeks after DMBA/TPA-treatment, cells were isolated from mice back skin. For each sample, skin cells were pooled from three mice. Skin cells were stained with biotin conjugated anti-mouse CD45.2 mAb, and then stained with barcode sequence-conjugated PE Streptavidin (TotalSeq™-A0951, BioLegend). CD45+ and CD45- cells were sorted by cell soter, and mixed in 1:1 ratio. For naive mice sample, CD45+ cells from WT and Cd226-/- mice were pooled, CD45- cells from WT and Cd226-/- mice were pooled, in 1:1 ratio. Viability of all samples were more than 70%. Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v3.1 (10X Genomics, PN-1000128), and Chromium Next GEM Chip G Single Cell Kit (PN-1000127, 10X Genomics), and the TotalSeq™-A Antibodies with 10x Single Cell 3' Reagent Kit v3.1 (BioLegend) as per the manufacturer’s protocol. The sequencing of libraries was performed at Macrogen Japan (Kyoto, Japan) using an Illumina HiSeq X. Processed files were generated from Cell Ranger (10X Genomics) pipeline.

first: Kazumasa

last: Kanemaru

first: Rikito

last: Murata

first: Akira

last: Shibuya

first: Kazuko


title: SIX6 regulation in human optic vesicles is mediated by early microenvironmenta factors

city: La Jolla

first: Karl

last: Wahlin

address: 9415 Campus Point Dr., #0946

department: Ophthalmology

institute: UC San Diego

summary: Human pluripotent stem cells (PSCs) represent an exciting tool to investigate the mechanisms of human eye development and to build models of human retinal disease. When grown in 3D, these cells can self-organize into laminar organized retinas; however, significant variation in the size, shape and composition of individual organoids exists, and this variation can create challenges. Neither the microenvironment nor the timing of critical growth factors driving eye formation or retinogenesis are fully understood. To explore the dynamics of early retinal organoid development, we have developed a SIX6-GFP reporter line that enables the systematic optimization of early eye field development, allowing for the identification of conditions that favor optic development. We found that SIX6 expression in 3D optic structures is influenced by small molecules regulating SHH and WNT signaling in a dose and time dependent fashion. In addition, we demonstrated that hypoxic growth conditions favor SIX6 expression, and promote eye formation. The systematic optimization of these pathways leads to optic vesicles with robust SIX6 expression and global gene expression profiles consistent with a retinal identity. The use of stem cell derived human retinal organoids with a real time marker for retinogenesis, therefore, represents an important model for probing the mechanisms of early human eye development.

overall_design: Day 35 retina cups were pooled (n=10-12) and separated as either GFP+ (n=2) or GFP- (n=3) samples and compared to human stem cells (n=2) (total of 7 samples run for RNA-seq).

first: Jie

last: Cheng

first: Melissa

last: Jones

first: Anna

last: Ogata

first: Nawal

last: Kibria

first: Sunayan

last: Ray

first: Kiara

last: Eldred

first: Catherine

last: Kim

first: Jacob

last: Heng

first: Robert

last: Johnston

first: Jenny

last: Phillips

first: David

last: Gamm

first: Cindy

last: Berlinicke

first: Donald

last: Zack


title: Transcriptomic analysis of lung cancers arising following deletion of Tp53, Rb1 and overexpression of MYC in distinct adult mouse lung eptithelial cell lineages

city: Melbourne

first: Daniel

middle: James

last: Gough

state: Victoria

address: 27-31 Wright Street, Clayton

department: Centre for Cancer Research

country: Australia

institute: Hudson Institute of Medical Research

summary: Profile of the transcriptomics of tumours arising in the mouse lung following deletion of Rb1, Trp53 and overexpression of MYC from neuroendocrine cells, club cells, AT2 cells or throughout the lung epithelium.

overall_design: Cell lines were generated from primary tumour masses. RNA was extracted from early passage cell lines. 1ug of RNA was used to generate sequencing libraries and sequencing runs performed in paired end mode obtaining 150 base pair reads at a depth of at least 20 million reads. QC was checked with FastQC and FastQ files aligned to mouse genome assembly GRC38 using Hisat2 and TPM quantified using stringtie/prepDE.


title: Study the differential gene expression of C57/BL6 Mouse tumors treated with EZH2 inhibitor GSK343 II

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: The study evaluated the differential gene expression in control Antibody or Ant-CXCL10 antibody injected mouse when compared to EZH2 inhibitor GSK343 treated mice tumors Briefly, control Antibody or Ant-CXCL10 antibody injected C57BL/6 mouse were treated with or without GSK343were analyzed for RNA-seq

overall_design: Total RNA was extracted from C57/BL6 mouse tumors, followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 2500 platform, with three biological replicates for each transformed sample.

first: Suresh

last: Bugide


title: Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing

city: Dalian

first: Wenqian

last: Song

address: Yan'an Road

institute: Dalian Blood Center

summary:
Objectives: To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT).
Methods: DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) genotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. The paternity testing parameters were attributed to each case quantitatively.
Results: The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699-99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation.
Conclusions: Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.

overall_design: A total of 14 cffDNA samples were analyzed by Y-chromosome mini-STR-based NGS.


title: Bulk RNA sequencing of airway organoids in differentiation medium towards ciliated cells

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

summary: Bulk RNA sequencing was performed on 3D airway cultures in airway organoid expansion medium and differentiation medium (CilM)

overall_design: RNA was extracted from 3D airway organoids cultures that were either grown in expansion conditions (AO) or differentiation conditions (CilM) for 21 days. After this, RNA was collected.

first: Lena

last: Böttinger

first: Norman

last: Sachs

first: Harry

last: Begthel

first: Jeroen

last: Korving

first: Marco

last: Viveen

first: Kerem

last: Eitan

first: Alex

last: Gilleles-Hillel

first: Hans

last: Clevers


title: A novel reprogramming strategy to generate functionally competent human hepatocytes [Illumina methylation]

city: Beijing

first: Bingqing

last: Xie

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

summary: Cell fate can be directly converted between differentiated cells by lineage reprogramming, thus generating multiple cell types across developmental lineages. However, lineage reprogramming is hindered by incomplete cell-fate conversion with residual initial cell identity and partial functions compared with the native counterparts. Here, we develop a high-fidelity reprogramming strategy, by mimicking the natural cell-fate changing route, thus permitting the production of functionally competent human hepatocytes from another cell type. We first converted fibroblasts into plastic hepatic progenitor-like cells (hHPLCs) and chemically induced them into mature hepatocytes. The molecular identity of human induced hepatocytes (hiHeps) are suggested a terminally differentiated state, resembling primary human hepatocytes (PHHs). Functionally, hiHeps were competent to replace PHHs for equivalent drug-metabolizing activities, toxicity prediction and hepatitis B virus infection. Remarkably, the stably robust expansion of hHPLCs allowed large-scale generation of mature hepatocytes. Our results demonstrate the necessity of taking a reprogramming step for plastic progenitors for efficient cell-fate conversion. This strategy is promising for the generation of other mature human cell types.

overall_design: Total of 9 samples were analyzed, which included human embryonic fibroblasts, primary human hepatocytes and human induced hepatocytes. Global methylation profiles of these cells were analyzed by microarray.

first: Da

last: Sun

first: Hongkui

last: Deng


title: Decoding Expression Dynamics of Protein and Transcriptome at the Single Cell Level through Multi-Omics Sequencing in Paired Picoliter Chambers

city: Xiamen

first: Xing

last: Xu

state: Fujian

address: 422 Road, Siming District, Xiamen, China

institute: Xiamen University

summary: Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for high-throughput cellular indexing of mRNAs and proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization (>95%). Combined with pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection. The picoliter reaction chambers allow higher detection sensitivity and lower sequencing cost. By using multi-Paired-seq, more elaborate classifications of breast cancers are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multi-modal measurements at the single cell level, which offers a new tool for cell biology, developmental biology, drug discovery and precision medicine.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles of different cancer cell lines.

first: Mingxia

last: Zhang

first: Xuebing

first: Chaoyong

last: Yang


title: Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma but can be subverted by enhancer hijacking of MYC or MYCN (CUT&RUN-Seq)

first: Richard

last: Young

overall_design: CUT&RUN-Seq against transcription factors in neuroblastoma cell line BE2C

first: Mark

last: Zimmerman

first: Adam

last: Durbin

first: Shuning

last: He

first: Alla

last: Berezovskaya

first: Felix

last: Oppel

first: Hui

last: Shi

first: Ting

last: Tao

first: Zhaodong

last: Li

first: Yu

last: Liu

first: Jinghui

first: Brian

last: Abraham

first: A

last: Look


title: The impaired quorum sensing response of MexAB-OprM efflux pump overexpressing mutants is not due to non-physiological efflux of 3-oxo-C12-HSL

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Multidrug (MDR) efflux pumps are ancient and conserved molecular machineries with relevant roles in different aspects of the bacterial physiology, besides antibiotic resistance. In the case of the environmental opportunistic pathogen Pseudomonas aeruginosa, it has been shown that overexpression of different efflux pumps is linked to the impairment of the quorum sensing (QS) response. Nevertheless, the causes of such impairment are different for each analyzed efflux pump. Herein, we performed an in-depth analysis of the QS-mediated response of a P. aeruginosa antibiotic resistant mutant that overexpresses MexAB-OprM. Although previous work claimed that this efflux pump extrudes the QS signal 3-oxo-C12-HSL, we show otherwise. Our results evidence that the observed attenuation in the QS response when overexpressing this pump is related to an impaired production of alkyl quinolone QS signals, likely prompted by the reduced availability of one of their precursors, the octanoate. Together with previous studies, this indicates that, although the consequences of overexpressing efflux pumps are similar (impaired QS response), the underlying mechanisms are different. This ‘apparent redundancy' of MDR efflux systems can be understood as a P. aeruginosa strategy to keep the robustness of the QS regulatory network and modulate its output in response to different signals.

overall_design: Differential gene expression in the Pseudomonas aeruginosa MexAB-OprM overexpressing mutant, mexR*, along the exponential and early stationary growth phase.

first: Manuel

last: Alcalde-Rico

first: Jorge

last: Olivares

first: Nigel

last: Halliday

first: Miguel

last: Cámara

first: José

middle: L

last: Martínez


title: Landscape of m6A modification in haematopoietic system unveils an essential role of IGF2BP2 in preserving haematopoietic stem cell function

city: Wuhan

first: jiwei

last: chang

state: Hubei

address: No.185, East Lake Road, Wuchang District,

department: Medical Research Institute,  School of Medicine,

institute: Wuhan University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is an abundant modification on mRNA, and plays critical functions in various cellular processes, including cell fate determination and lineage transition. However, the landscape and dynamics of m6A modification in haematopoietic system remain unknown. Here, we delineate a comprehensive m6A landscape across haematopoietic hierarchy and uncover that IGF2BP2 is required for preserving haematopoietic stem cells (HSCs) function. Our data reveal a marked cell-type- and haematopoietic-lineage-specific m6A landscape. Intriguingly, most m6A modifications arise in the early stat of haematopoiesis, and are critical in defining cellular states of HSCs. Moreover, m6A modification is the major factor in determining mRNA abundance in HSCs. Importantly, we find that higher expression of m6A reader IGF2BP2 is critical in controlling gene expression states and the functional maintenance of HSCs. IGF2BP2 deficiency induces apoptosis and quiescence loss, and substantially impairs the reconstitution capacity of HSCs. In addition, deletion of IGF2BP2 increases the mitochondrial activity of HSCs. Mechanistically, IGF2BP2 stabilizes Bmi1 mRNA in an m6A-dependent manner, which represses the expression of mitochondria-related genes. Collectively, our results present a fascinating portrait of m6A modification during haematopoiesis, and uncover a key role of IGF2BP2 in maintaining HSCs function by regulating Bmi1 stability and restraining mitochondrial activity.

overall_design: input samples: RNA-seq of 16 haematopoietic cell types; IP samples: Anti-m6A antibody IP RNA-seq of 16 haematopoietic cell types; Mettl3 input samples: RNA-seq of 7 haematopoietic cell types; Mettl3 IP samples: Anti-m6A antibody IP RNA-seq of 7 haematopoietic cell types; RNA-seq data of Igf2bp2 wild-type and knockout samples of LT.HSC.; Slam-seq for RNA transcription ratio: Slam-seq for 6 haematopoietic cell types; Slam-seq for RNA decay: Slam-seq for LT.HSC and MkP at 0.5h, 1h, 3h, 6h, 9h, 12h, 24h;

first: Haojian

last: Zhang

first: Rong

last: Yin

first: Jiwei

last: Chang


title: Transcriptome analysis of sheep oviduct epithelial cells under the  estrogen treatments

city: Hohhot

first: Xiao

middle: dan

address: Xinhuadajie 005

institute: Inner Mongolia Medical University

summary: Object:To study the effect of estrogen on fallopian tube function by comparing the gene expression of fallopian tube epithelial cells at different time of estrogen treatments. Method:The fallopian tube epithelial cells were cultured in vitro and treated with estrogen (E2) for different times (1.5h/3.5h/5.5h) before transcriptome sequencing  in triplicate.Valid data were obtained after quality evaluation, the Illumina Hiseq4000 is used for sequencing.Valid data is compared with the reference genome of the species, and statistics are performed separately according to the gene location information specified by the genome annotation files (gtf and gff). Result: The valid ratio(reads) of valid data > 94%, Q20 >99%, Q30% >96%.Valid Data for reference genome mapping, in all samples mapped reads >91% . Among them, the Exon (exon) region has the highest percentage of mapped reads.

overall_design: The sample includes three treatment time groups, and a control group, each with 3 replicates.

first: Xiaodan

first: Guifang

last: Cao


title: Identification of Genes Related to Growth Traits from Transcriptome Profiles of Duck Breast Muscle Tissue

status: Public on Oct 24 2021

first: Zhixiu

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

summary: The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to growth of duck skeletal muscle. RNA-sequencing technology was used to com-pare the transcriptome of duck breast muscles in an F2 population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be ex-pressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified be-tween the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the FABP3 and MYL4 involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks, and provided a theoretical basis for improving duck production and breeding of ducks.

overall_design: RNA-sequencing technology was used to compare the transcriptome of duck breast muscles in an F2 population with the high breast muscle rate (HB) and the low breast muscle rate (LB).

first: Wenshuang

last: Liang

first: Guobin

first: Guohong

last: Chen


title: Chromatin accessibility of TGFβ target genes determines the efficiency of hemogenic endothelial specification by RUNX1

city: PHILADELPHIA

first: Kai

last: Tan

state: Pennsylvania

address: 3501 CIVIC CENTER BLVD

institute: Children's Hospital of Philadelphia

summary: Epigenome and transcriptome characterization of endothelial cells following RUNX1 overexpression.

overall_design: Examination of transcriptome, chromatin accessibility, and histone modifications in endothelial cells subjected to overexpression of RUNX1 at different developmental timepoints.

first: Elizabeth

last: Howell

first: Peng

last: Gao

first: Nancy

last: Speck


title: Rapid pathogen-specific recruitment of immune effector cells in the skin by secreted toxins

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary:
Swift recruitment of phagocytic leukocytes is critical to prevent infection when bacteria breach through the protective layers of the skin. According to canonical models, this occurs via an indirect process that is initiated by contact of bacteria with resident skin cells and which is independent of the pathogenic potential of the invader. Here, we describe a more rapid mechanism of leukocyte recruitment to the site of intrusion of the important skin pathogen Staphylococcus aureus that is based on direct recognition of specific bacterial toxins, the phenol-soluble modulins (PSMs), by circulating leukocytes. This early recruitment was dependent on the transcription factor EGR1 and significantly contributed to the prevention of infection. Our findings refine the classical notion of the non-specific
and resident cell-dependent character of the innate immune response to bacterial infection by demonstrating a pathogen-specific high-alert mechanism involving direct recruitment of immune effector cells by secreted bacterial products.

overall_design: time series human PMN and various treatments

first: Thuan

last: Nguyen

first: Gordon

middle: Y

last: Cheung

first: Kevin

last: Rigby

first: Olena

last: Kamenyeva

first: Juraj

last: Kabat

first: Daniel

middle: E

first: Amer

last: Villaruz

first: Ryan

last: Liu

first: Pipat

last: Piewngam

first: Adeline

last: Porter

first: Saba

last: Firdous

first: Janice

last: Chiou

first: Matthew

last: Park

first: Rachelle

last: Hunt

first: Fawas

middle: M

last: Almufarriji

first: Vee

first: Titus

last: Asiamah

first: Joshua

last: McCausland

first: Emilie

last: Fisher

first: Anthony

last: Yeh

first: Justin

middle: S

last: Bae

first: Scott

last: Kobayashi

first: Ji Ming

last: Barber

first: Frank

last: DeLeo

first: Michael

last: Otto


title: Analysis of methylation in patients with systemic lupus erythematosus.

city: Changsha

first: Zhenghao

last: He

address: 139 Renmin Middle Road

institute: Second Xiangya Hospital, Central South University

summary: We collected the blood of 4 SLE patients and 4 normal people, and used magnetic beads to select B cells. The selected B cells were analyzed by methylation array.

overall_design: This study included B cell methylation data from four SLE patients and four normal controls.

first: Lu

last: Qianjin

first: Wu

last: haijing


title: Porphyromonas gingivalis W83:Transcriptome profiling and functional verification of flavodoxin

city: Chengdu

first: Peiyao

last: Wu

address: Renmin South road

institute: Sichuan University

summary: The aim of the study was to identify the role of flavodoxin gene in the virulence of P. gingivalis W83.The mRNA profiles of P. gingivalis W83 and flavodoxin mutant strain were generated by deep sequencing, in triplicate, using Illumina sequencing platform. Differential expression analysis of two groups (Three biological replicates per group) was performed using the DESeq R package. In total, 376 genes met the DEGs criteria (194 upregulated genes and 182 down-regulated genes). The KEGG pathway analysis indicated the DEGs were significantly enriched in three KEGG pathways, comprising pathways associated with Peroxisome, Two-component system and Quorum sensing.Importantly, we found that the flavodoxin gene can regulate the type IX secretion system and oxidative stress system in P. gingivalis W83. The knowledge obtained will help us to deeply understand the role of flavodoxin gene in the P. gingivalis W83 genome.

overall_design: Comparative transcriptomic analysis on the P. gingivalis W83 and the flavodoxin mutant strain

first: Jinmei

last: Zhang

first: Yafei

first: Lei

last: Zhao


title: Joint analysis of transcriptome and metabolome reveals the anti-low temperature mechanism of Hosta ventricosa

city: Jilin

first: chen

last: shaopeng

address: 77 Hanlin Road, Economic and Technological Development Zone, Jilin City, Jilin Province

institute: Jilin Agricultural Science and Technology College

summary: In this study, a total of 12,059 differential genes and 131 differential metabolites were obtained, and they were mainly concentrated in signal transduction and phenylpropane metabolic pathways. In the process of low temperature signal transduction, the hosta is mainly through the ion channels on the three cell membranes of COLD, CNGCs and CRLK to transmit Ca2+ inside and outside the cell to sense temperature changes, and stimulate SCRM to combine with DREB through the MAPK signal pathway and Ca2+ signal sensors such as CBL. Strengthen the low temperature resistance of the purple calyx hosta. The phenylpropane metabolic pathway and the flavonoid metabolism pathway are the main metabolic pathways for the hosta to resist low temperature stress. The hosta protects itself from low temperature damage by increasing the content of Genistein, Scopolentin and Scopolin. It is speculated that the hosta also adjusts Sinapyl alcohole and Coniferyl alcohol content ratio can change the morphological structure of cell wall and enhance low temperature resistance.

overall_design: Transcriptome comparison between samples treated at 3°C for 7 days and samples treated at 25°C at room temperature

first: QianQian

last: Zhuang

first: Shaopeng

last: Chen

first: ZhiXin

last: Ju


title: Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb

city: Seattle

first: Tyler

last: Hether

state: WA

address: 530 Fairview Ave N

department: Translational Sciences

institute: NanoString Technologies, Inc.

summary: Anosmia, the loss of smell, is a common and often the sole symptom of COVID-19. The onset of the sequence of pathobiological events leading to olfactory dysfunction remains obscure. Here, we have developed a postmortem bedside surgical procedure to harvest endoscopically samples of respiratory and olfactory mucosae and whole olfactory bulbs. Our cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling us to catch the virus while it was still replicating. We found that sustentacular cells are the major target cell type in the olfactory mucosa. We failed to find evidence for infection of olfactory sensory neurons, and the parenchyma of the olfactory bulb is spared as well. Thus, SARS-CoV-2 does not appear to be a neurotropic virus. We postulate that transient insufficient support from sustentacular cells triggers transient olfactory dysfunction in COVID-19. Olfactory sensory neurons would become affected without getting infected.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: One sample, olfactory mucosa of COVID case #8 containing six serial 6 µm cryosections.

first: Mona

last: Khan

first: Seung-Jun

last: Yoo

first: Marnick

last: Clijsters

first: Wout

last: Backaert

first: Arno

last: Vanstapel

first: Kato

last: Speleman

first: Charlotte

last: Lietaer

first: Su-Min

last: Choi

first: Ayse

last: Dereli

first: Lukas

last: Marcelis

first: Liuliu

last: Pan

first: Jason

last: Reeves

first: Pauline

last: Van Bulck

first: Hai

last: Zhou

first: Marc

last: Bourgeois

first: Yves

last: Debaveye

first: Paul

last: De Munter

first: Jan

last: Gunst

first: Mark

last: Jorissen

first: Katrien

last: Lagrou

first: Natalie

last: Lorent

first: Arne

last: Neyrinck

first: Marijke

last: Peetermans

first: Dietmar

last: Rudolf Thal

first: Christophe

last: Vandenbriele

first: Joost

last: Wauters

first: Peter

last: Mombaerts

first: Laura

last: Van Gerven


title: Blood-borne macrophages contribute to Alzheimer's disease modification through a TREM2-independent pathway

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Microglia and monocyte-derived macrophages (MDM) are key players in coping with Alzheimer's disease (AD). In amyloidosis mouse models, activation of microglia was found to be TREM2-dependent. Here, using Trem2-/-5xFAD mice, we assessed whether MDM act via a TREM2-dependent pathway. We adopted a treatment protocol targeting the programmed cell death ligand-1 (PD-L1) immune checkpoint, previously shown to modify AD via MDM involvement. Blocking PD-L1 in Trem2-/-5xFAD mice resulted in cognitive improvement and reduced levels of water-soluble amyloid beta (Aβ)1-42 with no effect on amyloid plaque burden. Single-cell RNA sequencing revealed that MDM, derived from both Trem2-/- and Trem2+/+5xFAD mouse brains, express a unique set of genes encoding scavenger receptors (e.g. Mrc1, Msr1). Blocking monocytes trafficking using anti-CCR2 antibody completely abrogated the cognitive improvement induced by anti-PD-L1 in Trem2-/-5xFAD mice, and similarly but to lower extent in Trem2+/+5xFAD mice. These results highlight a TREM2-independent disease-modifying activity of MDM in amyloidosis mouse model.

overall_design: Indicated cell types were isolated from the brains of TREM2+/+ or TREM2-/- 5xFAD mice. Cells were sorted and single-cell libraries of cell transcripts were sequenced.

first: Raz

last: Dvir-Szternfeld

first: Giulia

last: Castellani

first: Michal

last: Arad

first: Liora

last: Cahalon

first: Sarah

middle: P

last: Colaiuta

first: Hadas

last: Keren-Shaul

first: Tommaso

last: Croese

first: Chiara

last: Burgaletto

first: Kuti

last: Baruch

first: Tyler

last: Ulland

first: Marco

last: Colonna

first: Assaf

last: Weiner

last: Schwartz


title: Aberrant gene expression leakage from linage-specific heterochromatic loci during senescence [ChIP-seq]

status: Public on Oct 23 2021

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: To understand induction of cornification genes during lineage appropriate (keratinocyte differentiation) and inappropriate (fibroblast senescence) conditions , we generated histone modification and gene expression datasets. Then we compared keratinocyte's datasets with fibroblast senescence ones in this study.

overall_design: ChIP-seq datasets were generated for growing and senescent (RAS-induced) IMR90 cells.

first: Masako

last: Narita


title: Aberrant gene expression leakage from linage-specific heterochromatic loci during senescence [RNA-seq]

overall_design: RNA-seq datasets were generated for control and p16-senescence IMR90 cells, as well as control and RAS-induced senescence keratinocytes.


title: Global mouse gene expression data from  Idh2R140Q/NHD13 DN1/DN2 T-ALL, SCL/LMO1 non-DN1/DN2 T-ALL, and Wild Type samples assessed by oligonucleotide microarrays

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

summary:
Mutations in the isocitrate dehydrogenase 1 (IDH1) and IDH2 genes are frequently observed in a wide variety of hematologic malignancies, including myeloid and T-cell leukemias. In this study, we generated Idh2R140Q transgenic mice to examine the role of the Idh2R140Q mutation in leukemia. No leukemia developed in Idh2R140Q transgenic mice, suggesting a need for additional genetic events for leukemia development. Since myeloid cells from NUP98-HOXD13 fusion (NHD13) transgenic mice frequently acquire somatic Idh mutations when they transform to AML, we generated Idh2R140Q/NHD13 double transgenic mice. Idh2R140Q/NHD13 transgenic mice developed an immature T cell leukemia with an immunophenotype similar to double-negative 1 (DN1) or DN2 thymocytes. Idh2R140Q/NHD13 leukemic cells were enriched for an early thymic precursor transcriptional signature, and the gene expression profile for Idh2R140Q/NHD13 DN1/DN2 T-ALL closely matched that of human early/immature T cell precursor (EITP) ALL. Moreover, recurrent mutations found in EITP ALL patients, including KRAS, PTPN11, JAK3, SH2B3, and EZH2 were also found in Idh2R140Q/NHD13 DN1/DN2 T-ALL. In vitro treatment of Idh2R140Q/NHD13 thymocytes with enasidenib, a selective inhibitor of mutant IDH2, led to a marked decrease in leukemic cell proliferation. These findings demonstrate that Idh2R140Q/NHD13 mice can serve as a useful in vivo model for the study of EITP ALL development and therapy.
We used gene expression arrays to compare the global gene expression profiles between Idh2R140Q/NHD13 DN1/DN2 T-ALL, non-DN1/DN2 cortical T-ALL (CD4+CD8+) and wild-type thymus.

overall_design: For comparison between expression profiles of the three mouse genotypes we used Idh2R140Q/NHD13 DN1/DN2 T-ALL (N=9), non-DN1/DN2 cortical T-ALL (CD4+CD8+) (N=6) from SCL-LMO1 mice and wild-type thymus (N=3).

first: Liat

last: Goldberg

first: Vijay

last: Negi


title: Aberrant gene expression leakage from linage-specific heterochromatic loci during senescence

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptome Profiling of the Whole Blood of Dairy Cattle Differing in Milk Protein Yield

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: We functionally analyzed the blood transcriptomes from low- and high- milk protein yield to identify differences that might contribute to variation in milk production and quality.

overall_design: RNA-seq was performed on the whole blood of 8 low RFI and 8 high RFI animals to obtain transcriptomes for functional analysis using bioinformatics.

first: Xuehui

last: Wu

first: Jianxin

last: Liu


title: Early T follicular helper cell activity accelerates HCV-specific B cell expansion

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Early appearance of neutralizing antibodies during acute hepatitis C virus (HCV) infection is associated with spontaneous viral clearance. However, the longitudinal changes in antigen-specific memory B cell (MBC) responses associated with divergent HCV infection outcomes remain undefined. We characterized longitudinal changes in E2 glycoprotein-specific MBCs from subjects that either spontaneously resolved acute HCV infection or progressed to chronic infection using single cell RNA-seq and functional assays. HCV-specific antibodies in plasma from chronically infected subjects recognized multiple E2 genotypes, while those from spontaneous resolvers exhibited variable cross-reactivity to heterotypic E2. E2-specific MBCs from spontaneous resolvers peaked early after infection (4–6 months), following expansion of activated circulating T follicular helper cells (cTfh) expressing interleukin 21. In contrast, E2-specific MBCs from chronically infected subjects, enriched in VH1-69, expanded during persistent infection (> 1 year), in the absence of activated cTfh expansion. Early E2-specific MBCs from spontaneous resolvers produced monoclonal antibodies (mAbs) with fewer somatic hypermutations and lower E2 binding but similar neutralization as mAbs from late E2-specific MBCs of chronically infected subjects. These findings indicate that early cTfh activity accelerates expansion of E2-specific MBCs during acute infection, which might contribute to spontaneous clearance of HCV.

overall_design: Comparison of global gene expression in E2-specific memory B cells between individuals who resolve acute HCV infection (72 cells from 3 individuals - SR-4 (15), SR-2 (21), SR-6 (36) vs. those who develop persistent infection.(108 cells from 3 individuals - CI-5 (33), CI -3 (17), CI-9 (58))

first: Eduardo

last: Duron

first: Arash

last: Grakoui

first: Steven

last: Bosinger

first: Amit

last: Upadhyay


title: Omeprazole regulates miRNA, mRNA and lncRNA networks revealed by RNA deep-sequencing  in Barrett's Esophagus

city: Shanghai

first: Hua

last: Xiong

state: 上海市

address: Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute,Shanghai, Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China

institute: Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Recent clinical studies indicated Proton-pump inhibitors (PPIs) but not H2 Receptor Antagonists were associated with a decreased risk of esophageal adenocarcinoma. We’d like to clarify whether PPIs interfere with Barrett’s esophagus(BE) pathogenesis during BE treatment and explore the novel roles of omeprazole beyond acid suppression. RNA deep-sequencing was conducted in BE organoids exposed to periodic bile acids(400µM, pH 5.5) stimulation with or without omeprazole（40µM）treatment. A total of 129 long non-coding RNAs, 20 microRNAs, and 285 mRNAs were significantly regulated. Then, bioinformatics tools and databases were employed to explore the potential functions and relationships of these RNAs. Our data showed that the most significantly involved pathways modulated by omeprazole were Phenylalanine metabolism and Glycosaminoglycan biosynthesis - keratan sulfate. In addition, the miRNA-mRNA-lncRNA network regulated by omeprazole was constructed. We have demonstrated some novel acid-independent mechanisms of omeprazole that might yield valuable insight into clinical management of BE, irrespective of acid reflux symptoms.

overall_design: RNA deep-sequencing was conducted in BE organoids exposed to periodic bile acids (400µM, pH 5.5) stimulation with or without omeprazole (40µM) treatment.

first: Jiao

last: Huang


title: Transcriptome changes after TSG-6 treatment of mouse liver fibrosis.

city: Xi'an

first: min

last: wang

state: Shaanxi

address: 169 West Changle Road

institute: Fourth military medical university

summary: Our previous studies revealed that exogenous administration of TSG-6 can ameliorate liver fibrosis. We next analyzed liver transcriptome changes after TSG-6 treatment in order to explore possible therapeutic changes.

overall_design: Recombinant TSG-6 protein was given intravenously to the fibrotic mice and PBS was served as control. Three mice were used in each group. Two weeks later, mice liver RNA was extracted separately and then mixed equally. After that the RNA was labeled and hybridized to Agilent.

first: Min

last: Wang

first: Hao

last: Hu


title: A genome-wide analysis of expression differences during fiber initiation between Gossypium hirsutum and Gossypium barbadense

city: wuhan

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

summary: We compared different days post-anthesis (5DPA, 10DPA, 15DPA and 25DPA) differentially expressed genes (DEGs) in fiber development between G. hirsutum and G. barbadense. In addition, we analysis the differentially expressed genes (DEGs) function using the database for annotation, visualization and integrated discovery (DAVID). Overall, gene expression pattern have significantly difference between G. hirsutum and G. barbadense. In this study, G. barbadense DEGS in different two DPA are significantly more than G. hirsutum. In addation, there are 18937 DEGs were identified in fruit development and postembryonic development pathways and only upregulated in G. barbadense only. Taken together, these findings suggest that there are considerable differences of gene expression between G. hirsutum and G. barbadense in cotton fiber development different stages.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: Examination between Gossypium hirsutum and Gossypium barbadense

first: Quanjia

last: Chen

first: Dingming

last: Kang


title: Real-time quantitative PCR analysis of human EMT genes in MCF-7 cells [Data S9]

status: Public on Oct 22 2021

city: Boston

first: Naser

last: Jafari

state: MA

address: 72 East Concord

department: Hem Onc

institute: Boston University

summary:
Human EMT PCR array
PCR array data for expression of Cancer Stem Cell (CSC) genes in MCF-7 cells after treating with ND and T2D adipocytes EVs.

overall_design: MCF7 Cancer cells were treated with ND or T2D adipocytes exosomes for 5 days

first: Gerald

last: Denis


title: Mycobacterium tuberculosis hijacks host primary transcripts

summary: Intracellular pathogens requires efficient mechanism adapting the environment inside of host cells. Here we show that the transcriptomes of the cellular mycobacterium tuberculosis and of those released from the infected macrophage cells contain a large fraction of human transcripts by RNA polymerase II. Uptake of host pre-mRNAs is coincident with the co-localization of M. tuberculosis with nuclear membrane. The infective M. tuberculosis selectively uptakes snoRNAs.The intracellular pathogens has a preferable capability in taking pre-mRNAs. The host transcripts are not generally spliced nor translated.We suggest that the intracellular bacterium has acquired a mechanism to take transcripts from the host cell nuclus as its own nutrient supply and may help them to survive with hosts.

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172

overall_design: Totally 22 samples are analyzed. Intracellular and extracellular of MTB and BCG  in 6h and 24h were generated by deep sequencing separately, THP-1 infected by MTB and BCG in 6h and 24h were generated by deep sequencing separately, meanwhile uninfected control of THP-1 were generated. THP-1 were generated with two different library manner (polyA-capture and rRNA-removal).

first: Aizhen

last: Guo

first: Yi

last: Zhang


title: Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

summary: drugs targeting mitosis might affect the tumor microenvironment and sensitize cancer cells to immunotherapy. BAL101553 monotherapy increased survival in immune checkpoint blockade–resistant SB28 glioblastoma tumors and synergized with anti-CD40 antibody

overall_design: BAL treated mice vs ctrl

first: Vassilis

last: Genoud

first: Paul

last: Walker


title: EZH2 binds transcripts for splicing regulation and redistribution of H3K27me3 and H3K36me3 in prostate cancer cells

summary: PRC2 was found to bind to various RNAs, both noncoding RNA, coding RNA and nascent transcription RNA in ESCs. In order to determine the RNA binding profile and the binding characteristic in prostate cancer cells, through RIP-seq, we found out that EZH2 could associate with nascent transcripts in prostate cancer cells which have profound influence on the transcript splicing. What is more, we found that the H3K36me3 and H3K27me3 distribution in gene body region were regulated by EZH2 association with nascent transcripts.

overall_design: RIP-seq, ChIP-seq and RNA-seq was performed in androgen-dependent prostate cancer cells LNCaP (AD) and androgen-independent prostate cancer cells LNCaP (AI).


title: Real-time quantitative PCR analysis of human EMT genes in MCF-7 cells [Data S8]

summary:
Human EMT PCR array
PCR array data for expression of EMT genes in MCF-7 cells after treating with ND and T2D adipocytes EVs.


title: Adipocyte-derived extracellular vesicles promote breast cancer progression in type 2 diabetes


title: Real-time quantitative PCR analysis of MCF-7 cells after treating with TSP5-overexpressing cells' exosomes [Data S5]

summary:
Human EMT PCR array
Real-time quantitative PCR analysis of human EMT genes in PCR array data for expression of EMT genes in MCF-7 cells, upon treatment with exosomes released from TSP5-overexpressing human primary adipocytes (ND; ABM-007), compared to exosomes released from matched control adipocytes transduced with control lentiviral vector [Data S5]
PCR array data for expression of EMT genes in MCF-7 cells after treating with TSP5 overexpressing cells' exosomes

overall_design: Cancer cells were treated for 3 days to test the effect of exosomes' TSP5 on MCF7 cell


title: ARRDC4 knock out Mouse Heart Analysis

city: NY

first: Yoshinobu

last: Nakayama

state: NY

address: 160 Convent Ave

institute: City College of New York

summary: Comprehensive genetic analysis of Arrdc4 knockout hearts

overall_design: Wild type mouse hearts versus Knock-out mouse hearts, n=3 each

first: Jun

last: Yoshioka


title: Surface Lin28A Expression Consistent With Cellular Stress Parallels Indicators of Senescence

city: San Diego

first: Oscar

last: Echeagaray

state: CA

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

summary: Single-cell RNA-seq (10X Genomics Chromium) to profile Adult cardiac interstitial sorted based on the presence of Lin28 on cell membrane surface Lin28S+/-.

overall_design: Transcriptional profiling of  Adult cardiac interstitial sorted based on the presence of Lin28 on cell membrane surface Lin28S+/- by scRNA-Seq approaches using 10X Genomics Chromium

first: Mark

last: Sussman


title: Fatal enhanced respiratory syncytial virus disease in toddlers

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: This study perfromed RNAseq on two FFPE lung samples from deceased participants from the 1867 RSV vaccine trial and compared these data to age and race matched controls from LungMAP.

overall_design: RNA was extratced from FFPE slides using Illumina RNA Access.  Indexed, pooled libraries were then sequenced on the Illumina NextSeq 550 platform with high-output flow cell–producing stranded, single end reads (1× 75 bp). Comparisons were perfromed in R.


title: Real-time quantitative PCR analysis of human EMT genes in MCF-7 cells [Data S1]

summary:
Human EMT PCR array
PCR array data for expression of EMT genes in MCF-7 cells after co-culture with insulin sensitive (IS) and insulin resistant (IR) adipocytes

overall_design: Cancer cells were co coltured with adipocytes for 5 days to test the effect of insulin resistant adipocytesof MCF7 cell


title: Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

summary:
Purpose: Although the prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase, there is no effective treatment approved for this condition. We previously showed, in high-fat diet (HFD)-fed mice, that the supplementation of combined metabolic activators (CMA), including nicotinamide riboside (NAD+ precursor) and the potent glutathione precursors serine and N-acetyl-l-cysteine (NAC), significantly decreased fatty liver by promoting fat oxidation in mitochondria. Afterwards, in a one-day proof-of-concept human supplementation study, we observed that this CMA, including also L-carnitine tartrate (LCT), resulted in increased fatty acid oxidation and de novo glutathione synthesis. However, the underlying molecular mechanisms associated with supplementation of CMA have not been fully elucidated.
Conclusions: Our study demonstrated in hamsters that the chronic supplementation of this CMA (changing serine for betaine) at two doses significantly decreased hepatic steatosis. We further generated liver transcriptomics data and integrated these data using a liver-specific genome-scale metabolic model of liver tissue. We systemically determined the molecular changes after the supplementation of CMA and found that it activates mitochondria in the liver tissue by modulating global lipid, amino acid, antioxidant and folate metabolism. Our findings provide extra evidence about the beneficial effects of a treatment based on this CMA against NAFLD.

overall_design: In this study, we perfomed liver transcriptomics data on tissue samples obtained from control group and CMA-treated groups (HFD+MI_D1, HFD+MI_D2).

first: Jordi

last: Mayneris-Perxachs

first: Noemí

last: Boqué

first: Josep

last: del Bas

first: Lluís

last: Arola

first: Meng

last: Yuan

first: Hasan

last: Türkez

first: Mathias

last: Uhlén

first: Jan

last: Borén

first: Cheng

first: Adil

last: Mardinoglu

first: Antoni

last: Caimari


title: Transcriptome changes of endothelial cells in mouse tumor by Nf2/Merlin

status: Public on Oct 21 2021

city: Daejeon

first: Myung Jin

institute: Institute for Basic Science

summary: To investigate the trancriptomic changes of endothelial cells (ECs) by Nf2/Merlin, Lewis Lung Carcinoma (LLC) tumor ECs from Ctrl and NF2 KO mice were sorted by FACS and single-cell RNA seq was performed.

overall_design: Tumor endothelial cells of Ctrl and NF2 KO mice were sorted and single-cell RNA libraries were made.

first: Gou

last: Koh

first: Jung

middle: H

last: Bae

first: Myung

middle: J


title: Immunoglobulin enhancers increase RNA polymerase 2 stalling at somatic hypermutation target sequences [ChIP-Seq]

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: Bar-Ilan University

summary: Somatic hypermutation (SHM) drives the genetic diversity of immunoglobulin genes in activated B cells and supports the generation of antibodies with increased affinity for antigen. SHM is targeted to Ig genes by their enhancers (DIVACs; diversification activators) but how the enhancers mediate this activity is unknown. We show that DIVACs that strongly stimulate SHM increase the phosphorylation of RNA polymerase 2 (Pol2) and Pol2 occupancy in the mutating gene with little or no accompanying increase in elongation-competent Pol2 or production of full length transcripts, indicating the accumulation of stalled Pol2. DIVAC-induced stalling is weakly associated with an increase in the detection of single-stranded DNA bubbles in the mutating target gene. We did not find evidence for anti-sense transcription or an association of H3K27ac with DIVAC activity in the mutating gene. These findings argue for a connection between Pol2 stalling and cis-acting targeting elements in the context of SHM and thus define a mechanistic basis for locus-specific targeting of SHM in the genome. Our results suggest that DIVACs make the target gene a suitable platform for AID-mediated mutation without the need for increasing transcriptional output.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: 10 samples of ChIP-seq profiles in Ramos cell line, and 16 samples of ChIP-seq profiles in DT40 cell line including the Input controls

first: Tarsalainen

last: Alina


title: A pigtailed macaque model for Kyasanur Forest disease virus and Alkhurma hemorrhagic disease virus pathogenesis

city: Hamilton

first: Dan

last: Sturdevant

address: 903 S 4th street

institute: NIH

summary: Kyasanur Forest disease virus (KFDV) and the closely related Alkhurma hemorrhagic disease virus (AHFV) are emerging flaviviruses that cause severe viral hemorrhagic fevers in humans. Increasing geographical expansion and case numbers, particularly of KFDV in southwest India, class these viruses as a public health threat. Viral pathogenesis is not well understood and additional vaccines and antivirals are needed to effectively counter the impact of these viruses. However, current animal models for KFDV do not accurately reproduce viral tissue tropism or clinical outcomes observed in humans. Here, we show pigtailed macaques (Macaca nemestrina) infected with KFDV or AHFV develop viremia that peaks 2 to 4 days following inoculation. Over the course of infection, animals developed lymphocytopenia, thrombocytopenia, and elevated liver enzymes. Infected animals exhibited hallmark signs of human disease characterized by a flushed appearance, piloerection, dehydration, loss of appetite, weakness, and hemorrhagic signs such as epistaxis. Virus was commonly present in the gastrointestinal tract, consistent with human disease caused by KFDV and AHFV where gastrointestinal symptoms (hemorrhage, vomiting, diarrhea) are common. This work characterizes a nonhuman primate model for KFDV and AHFV that closely resembles human disease for further utilization in understanding host immunity and development of antiviral countermeasures.

first: Rebecca

last: Broeckel

first: Friederike

last: Feldmann

first: Kristin

last: McNally

first: Abhilash

middle: I

last: Chiramel

first: Gail

first: Jacqueline

last: Leung

first: Patrick

last: Hanley

first: Jamie

last: Lovaglio

last: Rosenke

first: Dana

last: Scott

first: Greg

last: Saturday

first: Fadila

last: Bouamr

first: Angela

last: Rasmussen

first: Shelly

last: Robertson

first: Sonja

last: Best


title: Analysis of tanscriptome reprogramming after knockdown of TET1 in cancer cell lines

city: Albuquerque

first: Steven

middle: A

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

summary: The effect of modulating TET1 expression on cell phenotype in vitro was characterized

overall_design: Total RNA isolated from TET1 knockdown and control cancer cell lines

first: Maria

last: Picchi

first: Piotr

last: Filipczak


title: Transcriptional profiling reveals an upregulation of genes related to Sphingolipid metabolism and Oxidative phosphorilation in HRas and NRas double-KO mice (DKO), which die because of a severe respiratory distress

city: Salamanca

first: Eugenio

last: Santos

address: Campus Miguel de Unamuno

department: Instituto de Biología Celular y Molecular del Cáncer

institute: Universidad de Salamanca y CBERONC

summary: We used microarrays to investigate gene expression changes in the lungs of Control, Hras-KO, Nras-KO and DKO mice. These DKO animals die at birth because of respiratory distress, caused by an impaired lung maturation. N-acetyl cysteine antenatal treatment ameliorates the newborn lethality.

overall_design: Manually selected lungs of Control, HRas-KO, NRas-KO and DKO from postnatal day 0 were used for RNA extraction using the TRIZOL protocol. RNA was further purified using Qiagen Rneasy mini kit. Each RNA sample for each microarray was obtained from one individual animal.

first: R

last: Fuentes-Mateos

first: A

last: Fernandez-Medarde

first: E


title: Next Generation Sequencing Facilitates Quantitative Analysis of  ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice [RNA-seq]

city: shenzhen

first: xin

last: dai

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

summary: Objective: the next generation sequencing (NGS) has revolutionized the system-based analysis of cellular pathways. The purpose of this study was to explore the mechanism of methylation changes caused by SAHH knockout and dietary betaine addition in atherosclerosis.

overall_design: Methods: Mouse vascular tissue mRNA profiles of ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice were generated by deep sequencing, in triplicate. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.20.0).

first: Xin

last: Dai


title: Glutaminyl cyclase (QC) activity affects gene expression in macrophages during inflammation

city: Taipei

first: Chen

middle: Yi

last: Ling

address: 128 Academia Road, Section 2

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Glutaminyl cyclase (QC) activity in macrophage cells is correlated with the gene expression of MCP-2 and QC-catalyzed N-terminal pGlu formation of MCPs is required for macrophage migration and provide new insights into the role of QC in the inflammation process.

overall_design:
In the study presented here, we found that 3,770 genes exhibited different expression level (> 1.7 folds) in response to the treatment of LPS, and that 4,124 genes showed different expression in response to the treatments of PBD150  inhibitor and LPS. The overlap between both conditions contained 602 genes, we identified 10 genes whose expression levels are significantly correlated with the pretreatment of PBD150 inhibitor.
27 samples: untreated control, LPS only treatment, and LPS and PBD150 QC inhibitor treatment

first: Yi-Ling

last: Chen

first: Andrew

last: Wang


title: Immunoglobulin enhancers increase RNA polymerase 2 stalling at somatic hypermutation target sequences [GRO-seq]

first: Yaakov

last: Maman

overall_design: 2 samples of GRO-seq profiles in DT40 cell line

first: Alina

last: Tarsalainen


title: HEK293T bulk RNA-Seq

city: San Francisco

first: Manuel

middle: D

last: Leonetti

address: 499 Illinois St 4th floor

institute: Chan Zuckerberg Biohub

summary: We report bulk RNA-sequencing from a HEK293T cell line grown under normal conditions.

overall_design: RNA-Seq analysis from biological triplicate experiment


title: Analysis of reprogramming of epigenome in TET1 knockdown cancer cell lines

summary: Epigenetic changes associated with knockdown of TET1 in 2 cancer cell lines was assessed

overall_design: Bisulphite converted DNA from the 4 samples were hybridized to the Illumina  HumanMethylation450k Beadchip. Delta change in Beta value in TET1 kd compared to parent cell lines was calculated


title: Gene expression changes in HEI-193 (NF2-deficient Schwannoma) cells by Nf18001 or TEW7197 treatment.

city: BUSAN

first: Bum-Joon

last: Park

address: Busandaehak-ro 63

department: Molecular Biology

institute: Pusan National University

summary:
Loss of NF2 (merlin) has been suggested as a genetic cause of neurofibromatosis type 2 and malignant peripheral nerve sheath tumor (MPNST). Previously, we demonstrated that NF2 sustained TGF- receptor 2 (TR2) expression and reduction or loss of NF2 activated non-canonical TGF- signaling, which reduced RKIP expression via TR1 kinase activity. Here, we show that a selective RKIP inducer (novel chemical, Nf18001) inhibits tumor growth and promotes schwannoma cell differentiation into mature Schwann cells under NF2-deficient conditions. In addition, Nf18001 is not cytotoxic to cells expressing NF2 and is not disturb canonical TGF- signaling. Moreover, the novel chemical induces expression of SOX10, a marker of differentiated Schwann cells, and promotes nuclear export and degradation of SOX2, a stem cell factor. Treatment with Nf18001 inhibited tumor growth in an allograft model with mouse schwannoma cells. These results strongly suggest that selective RKIP inducers could be useful for the treatment of neurofibromatosis type 2 as well as NF2-deficient MPNST.
To know the global effect of Nf18001, we performed the microarray with HEI-193.

overall_design: For differential gene expression analysis by Nf18001 and TEW7197 treatment, microarray was performed using the Affymetrix GeneChip (Human Gene 2.0 ST Array X 6; DNA Link, Inc, Korea). Total RNA obtained from HEI-193 treated with Nf18001 (1μM for 2, 4, 6 day or 2μM for 6 day) or TEW7197 10μM for 6 day) was quantified and used for analysis. For differentially expressed gene (DEG) analysis, probes were selected if the difference in expressions were 2 fold compared to the HEI-193 control, and were statistically filtered by t-test (p<0.05). For the functional analysis, only DEG probes were used. Web tool DAVID (david.abcc.ncifcrf.gov/home.jsp), data base of which are Gene Ontology, KEGG, BIOCARTA was used for functional grouping of probes. All statistical and functional analysis were performed by DNA Link, Inc.

first: Jung-Hyun

last: Cho

first: Soyoung

first: Soyeong

last: Kim

first: So-mi

last: Kang

first: Tae-Gyun

last: Woo

first: Min-Ho

last: Yoon

first: Hyunkee

last: Lee

first: Myeonggyo

last: Jeong

first: Yeong

first: Heegyu

first: Young

middle: T

last: Han

first: Young-Ger

last: Suh

first: Bae-Hoon

first: Yonghoon

last: Kwon

first: Hwayoung

last: Yun


title: Suppression of the CIC-DUX4 oncogene through p300/CBP inhibition

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: A recently identified pediatric subtype of undifferentiated round cell sarcoma that is driven by fusion between the cell cycle regulator and transcriptional repressor, capicula (CIC) and the transcriptional activator, DUX4 has been identified based on its histology, clinical differences, and aggressiveness. Because CIC-DUX4 acquires the p300-interacting activation domain of DUX4, we hypothesized that its transcriptional activation potential, and thus the oncogenicity of CIC-DUX4, would require p300 or its homologues, CBP.  Recently, a new class of histone acetyltransferase inhibitors with high selectivity for p300 and CBP has been described, and two compounds, A-485, and iP300w, have been shown to inhibit p300 and CBP both in vitro and in vivo with iP300w having the ability to reverse gene expression changes caused by DUX4.  If this hypothesis is correct, iP300w should potently counteract the CIC-DUX4 gene expression program and might be a particularly effective therapy for CDS. In this study, we confirm this hypothesis, demonstrating that CIC-DUX4 requires p300/CBP for its activity.  We also demonstrate that CIC-DUX4 induces a global increase in H3 acetylation, like DUX4, which is reversible with iP300w treatment.  We find that CIC-DUX4 activity is potently blocked by iP300w, and that this compound has potent activity against CDS cell lines and in an in vivo cancer xenograft assay.

overall_design: 3 replicates of  three treatment conditions by RNA-seq

first: Michael

last: Kyba

first: Darko

last: Bosnakovski


title: RNAseq analysis of blood from patients with Multisystem Inflammatory Syndrome in Children (MISC)

city: Los Angeles

first: Rebecca

middle: Amelia

last: Porritt

address: 8700 Beverly Blvd

department: Pediatrics

institute: Cedars Sinai

summary: RNAseq analysis of RNA extracted from blood of febrile controls and MISC patients

overall_design: RNA was extracted from blood of 13 febrile controls and 12 MISC patients. Library construction was performed using the SMARTer Stranded Total RNA-Seq Kit v3. Sequencing was performed on the NovaSeq 6000 (Illumina) using 2x50 bp sequencing.

first: Moshe

last: Arditi


title: Immunoglobulin enhancers increase RNA polymerase 2 stalling at somatic hypermutation target sequences

first: Yaakov

last: Maman

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Effects of maoto (ma-huang-tang) on transcriptome signature in influenza virus infection

city: Yoshiwara, Amimachi, Inachiki-gun

first: Akinori

last: Nishi

state: Ibaraki

department: Tsumura Kampo Research Laboratories

institute: Tsumura & Co.

summary: We evaluated the effects of maoto, a traditional kampo medicine, as a herbal multi-compound medicine on host transcriptome responses in a mouse model of influenza infection. On the fifth day of oral administration to mice intranasally infected with influenza virus (A/PR/8/34 (H1N1), maoto significantly improved survival rate, decreased viral titer, and ameliorated the infection-induced phenotype as compared with control mice. Analysis of the lung and plasma transcriptome profile showed that maoto significantly up-regulated the expression of macrophage- and T-cell-related genes. Collectively, these results suggest that maoto regulates the host’s inflammatory response.

overall_design: Materials  Maoto was dissolved in distilled water before administration to mice. Mouse-adapted influenza virus (A/PR/8/34(H1N1)) (PR8) was used to infect mice.   Virus culture  The influenza virus was cultured in Madin–Darby canine kidney (MDCK) cells, and PR8 collected from the culture medium was used for intranasal inoculation of mice.  Animals  Female BALB/c Cr Slc mice purchased from Japan SLC, Inc. (Shizuoka, Japan) were used from 6 weeks of age after habituation.   In vivo influenza virus inoculation  Influenza virus (1x10^5　PFU/0.05 mL/mouse) was administered by intranasal inoculation. Maoto (2 g/10mL/kg) was orally administered for 5 days starting 1 hour after inoculation. Mice with no inoculation were used as control mice against the infection, and infected mice that were treated distilled water were used as infected control mice. In total, there were three groups of mice: 1) no-inoculation (NI) group; 2) influenza virus inoculation (IVI) control group;  3) IVI with MT 2 g/10mL/kg treatment (IVI+MT) group. Ten mice from each of the three mouse groups were used to collect lung tissue  at 5 day post inoculation (dpi). In the result, the number of surviving mice in each group was 10/10(NI), 4/10 (IVI) and 9/10 (IVI+MT) at 5 dpi, and the lung tissue sample from these mice were used for transcriptome analysis.

first: Noriko

last: Kaifuchi

first: Chika

last: Shimobori

first: Katsuya

last: Ohbuchi

first: Seiichi

last: Iizuka

first: Aiko

last: Sugiyama

first: Keisuke

last: Ogura

first: Masahiro

last: Yamamoto

first: Haruo

last: Kuroki

first: Shigeki

last: Nabeshima

first: Ayako

last: Yachie

first: Yukiko

last: Matsuoka

first: Hiroaki

last: Kitano


title: mTORC1 promotes malignant large cell/anaplastic histology and is a therapeutically targetable vulnerability in SHH-TP53 mutant medulloblastoma

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

institute: Fondazione Human Technopole

summary: Distinct molecular subgroups and subtypes have been identified for medulloblastoma (MB), one of the most malignant brain tumors of childhood, with the sonic hedgehog (SHH)-activated subgroup of patients with mutations in p53 having a very severe outcome, associated with unfavorable histological large cell/anaplastic (LC/A) features. Aim of this study was to determine whether hyperactivation of mechanistic Target Of Rapamycin Complex 1 (mTORC1) pathway, whose role in molecular subtypes of MB is currently undefined, underlies the acquisition of LC/A histology in this subtype. MBs developing in p53-deficient Ptch+/- SHH mice show LC/A features that correlate with mTORC1 hyperactivation, which, mechanistically, is mediated by a decrease in the p53-dependent expression of the negative mTORC1 regulator Tsc2. Ectopic mTORC1 activation in mouse MB cancer stem cells (CSCs) promotes the acquisition of the LC/A phenotype. Furthermore, mTORC1 inhibition in both autochthonous p53-mutant SHH MBs and CSC-derived LC/A MBs results in reduced tumor burden and enhanced survival. Most remarkably, mTORC1 hyperactivation in tumor cells is detected only in human p53-mutant SHH MB samples and treatment with rapamycin of a human preclinical model phenocopying this subgroup decreases tumor growth and malignancy. As such, mTORC1 may act as a new and specific druggable target for this subset of SHH MB, thus resulting in the implementation of a more stringent MB risk stratification and in the potentially rapid translation of this precision medicine approach into the clinical setting.

overall_design: Gene espression profiles of Ptch1+/- MBs with or without p53 mutation were compared to identify gene signatures reminiscent of specific molecular subtypes of MBs

first: Valentina

last: Conti

first: Rossella

last: Galli